1
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Karmakar S, Patra S, Pramanik K, Adhikary A, Dey A, Majumdar A. Reactivity of Thiolate and Hydrosulfide with a Mononuclear {FeNO} 7 Complex Featuring a Very High N-O Stretching Frequency. Inorg Chem 2024; 63:8537-8555. [PMID: 38679874 DOI: 10.1021/acs.inorgchem.3c03274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2024]
Abstract
Synthesis, characterization, electronic structure, and redox reactions of a mononuclear {FeNO}7 complex with a very high N-O stretching frequency in solution are presented. Nitrosylation of [(LKP)Fe(DMF)]2+ (1) (LKP = tris((1-methyl-4,5-diphenyl-1H-imidazol-2-yl)methyl)amine) produced a five-coordinate {FeNO}7 complex, [(LKP)Fe(NO)]2+ (2). While complex 2 could accommodate an additional water molecule to generate a six-coordinate {FeNO}7 complex, [(LKP)Fe(NO)(H2O)]2+ (3), the coordinated H2O in 3 dissociates to generate 2 in solution. The molecular structure of 2 features a nearly linear Fe-N-O unit with an Fe-N distance of 1.744(4) Å, N-O distance of 1.162(5) Å, and
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Affiliation(s)
- Soumik Karmakar
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & 2B Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Suman Patra
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & 2B Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Koushik Pramanik
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & 2B Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Amit Adhikary
- Department of Chemistry, Technology Campus, University of Calcutta, JD Block, Sector III, Salt Lake, Kolkata 700098, India
| | - Abhishek Dey
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & 2B Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Amit Majumdar
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & 2B Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India
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2
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Araten AH, Brooks RS, Choi SDW, Esguerra LL, Savchyn D, Wu EJ, Leon G, Sniezek KJ, Brynildsen MP. Cephalosporin resistance, tolerance, and approaches to improve their activities. J Antibiot (Tokyo) 2024; 77:135-146. [PMID: 38114565 DOI: 10.1038/s41429-023-00687-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 10/23/2023] [Accepted: 11/05/2023] [Indexed: 12/21/2023]
Abstract
Cephalosporins comprise a β-lactam antibiotic class whose first members were discovered in 1945 from the fungus Cephalosporium acremonium. Their clinical use for Gram-negative bacterial infections is widespread due to their ability to traverse outer membranes through porins to gain access to the periplasm and disrupt peptidoglycan synthesis. More recent members of the cephalosporin class are administered as last resort treatments for complicated urinary tract infections, MRSA, and other multi-drug resistant pathogens, such as Neisseria gonorrhoeae. Unfortunately, there has been a global increase in cephalosporin-resistant strains, heteroresistance to this drug class has been a topic of increasing concern, and tolerance and persistence are recognized as potential causes of cephalosporin treatment failure. In this review, we summarize the cephalosporin antibiotic class from discovery to their mechanisms of action, and discuss the causes of cephalosporin treatment failure, which include resistance, tolerance, and phenomena when those qualities are exhibited by only small subpopulations of bacterial cultures (heteroresistance and persistence). Further, we discuss how recent efforts with cephalosporin conjugates and combination treatments aim to reinvigorate this antibiotic class.
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Affiliation(s)
- Alison H Araten
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Rachel S Brooks
- Department of English, Princeton University, Princeton, NJ, USA
| | - Sarah D W Choi
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Laura L Esguerra
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA
| | - Diana Savchyn
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA
| | - Emily J Wu
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA
| | - Gabrielle Leon
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA
| | - Katherine J Sniezek
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA
| | - Mark P Brynildsen
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA.
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3
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Srour B, Gervason S, Hoock MH, Monfort B, Want K, Larkem D, Trabelsi N, Landrot G, Zitolo A, Fonda E, Etienne E, Gerbaud G, Müller CS, Oltmanns J, Gordon JB, Yadav V, Kleczewska M, Jelen M, Toledano MB, Dutkiewicz R, Goldberg DP, Schünemann V, Guigliarelli B, Burlat B, Sizun C, D'Autréaux B. Iron Insertion at the Assembly Site of the ISCU Scaffold Protein Is a Conserved Process Initiating Fe-S Cluster Biosynthesis. J Am Chem Soc 2022; 144:17496-17515. [PMID: 36121382 PMCID: PMC10163866 DOI: 10.1021/jacs.2c06338] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Iron-sulfur (Fe-S) clusters are prosthetic groups of proteins biosynthesized on scaffold proteins by highly conserved multi-protein machineries. Biosynthesis of Fe-S clusters into the ISCU scaffold protein is initiated by ferrous iron insertion, followed by sulfur acquisition, via a still elusive mechanism. Notably, whether iron initially binds to the ISCU cysteine-rich assembly site or to a cysteine-less auxiliary site via N/O ligands remains unclear. We show here by SEC, circular dichroism (CD), and Mössbauer spectroscopies that iron binds to the assembly site of the monomeric form of prokaryotic and eukaryotic ISCU proteins via either one or two cysteines, referred to the 1-Cys and 2-Cys forms, respectively. The latter predominated at pH 8.0 and correlated with the Fe-S cluster assembly activity, whereas the former increased at a more acidic pH, together with free iron, suggesting that it constitutes an intermediate of the iron insertion process. Iron not binding to the assembly site was non-specifically bound to the aggregated ISCU, ruling out the existence of a structurally defined auxiliary site in ISCU. Characterization of the 2-Cys form by site-directed mutagenesis, CD, NMR, X-ray absorption, Mössbauer, and electron paramagnetic resonance spectroscopies showed that the iron center is coordinated by four strictly conserved amino acids of the assembly site, Cys35, Asp37, Cys61, and His103, in a tetrahedral geometry. The sulfur receptor Cys104 was at a very close distance and apparently bound to the iron center when His103 was missing, which may enable iron-dependent sulfur acquisition. Altogether, these data provide the structural basis to elucidate the Fe-S cluster assembly process and establish that the initiation of Fe-S cluster biosynthesis by insertion of a ferrous iron in the assembly site of ISCU is a conserved mechanism.
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Affiliation(s)
- Batoul Srour
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Sylvain Gervason
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Maren Hellen Hoock
- Fachbereich Physik, Technische Universität Kaiserslautern, Erwin-Schrödinger-Str. 56, 67663 Kaiserslautern, Germany
| | - Beata Monfort
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Kristian Want
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Djabir Larkem
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Nadine Trabelsi
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Gautier Landrot
- Synchrotron SOLEIL, L'Orme des Merisiers, BP48 Saint Aubin 91192 Gif-Sur-Yvette, France
| | - Andrea Zitolo
- Synchrotron SOLEIL, L'Orme des Merisiers, BP48 Saint Aubin 91192 Gif-Sur-Yvette, France
| | - Emiliano Fonda
- Synchrotron SOLEIL, L'Orme des Merisiers, BP48 Saint Aubin 91192 Gif-Sur-Yvette, France
| | - Emilien Etienne
- Aix Marseille Univ, CNRS, Laboratoire de Bioénergétique et Ingénierie des Protéines (BIP), 31 Chemin Joseph Aiguier, 13402 Marseille, France
| | - Guillaume Gerbaud
- Aix Marseille Univ, CNRS, Laboratoire de Bioénergétique et Ingénierie des Protéines (BIP), 31 Chemin Joseph Aiguier, 13402 Marseille, France
| | - Christina Sophia Müller
- Fachbereich Physik, Technische Universität Kaiserslautern, Erwin-Schrödinger-Str. 56, 67663 Kaiserslautern, Germany
| | - Jonathan Oltmanns
- Fachbereich Physik, Technische Universität Kaiserslautern, Erwin-Schrödinger-Str. 56, 67663 Kaiserslautern, Germany
| | - Jesse B Gordon
- Department of Chemistry, The Johns Hopkins University, 3400 N. Charles Street, Baltimore, Maryland 21218, United States
| | - Vishal Yadav
- Department of Chemistry, The Johns Hopkins University, 3400 N. Charles Street, Baltimore, Maryland 21218, United States
| | - Malgorzata Kleczewska
- Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Abrahama 58, 80-307 Gdansk, Poland
| | - Marcin Jelen
- Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Abrahama 58, 80-307 Gdansk, Poland
| | - Michel B Toledano
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Rafal Dutkiewicz
- Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Abrahama 58, 80-307 Gdansk, Poland
| | - David P Goldberg
- Department of Chemistry, The Johns Hopkins University, 3400 N. Charles Street, Baltimore, Maryland 21218, United States
| | - Volker Schünemann
- Fachbereich Physik, Technische Universität Kaiserslautern, Erwin-Schrödinger-Str. 56, 67663 Kaiserslautern, Germany
| | - Bruno Guigliarelli
- Aix Marseille Univ, CNRS, Laboratoire de Bioénergétique et Ingénierie des Protéines (BIP), 31 Chemin Joseph Aiguier, 13402 Marseille, France
| | - Bénédicte Burlat
- Aix Marseille Univ, CNRS, Laboratoire de Bioénergétique et Ingénierie des Protéines (BIP), 31 Chemin Joseph Aiguier, 13402 Marseille, France
| | - Christina Sizun
- Institut de Chimie des Substances Naturelles, CNRS, Université Paris Saclay, Avenue de La Terrasse, 91190 Gif-sur-Yvette, France
| | - Benoit D'Autréaux
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
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4
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Lehnert N, Kim E, Dong HT, Harland JB, Hunt AP, Manickas EC, Oakley KM, Pham J, Reed GC, Alfaro VS. The Biologically Relevant Coordination Chemistry of Iron and Nitric Oxide: Electronic Structure and Reactivity. Chem Rev 2021; 121:14682-14905. [PMID: 34902255 DOI: 10.1021/acs.chemrev.1c00253] [Citation(s) in RCA: 90] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Nitric oxide (NO) is an important signaling molecule that is involved in a wide range of physiological and pathological events in biology. Metal coordination chemistry, especially with iron, is at the heart of many biological transformations involving NO. A series of heme proteins, nitric oxide synthases (NOS), soluble guanylate cyclase (sGC), and nitrophorins, are responsible for the biosynthesis, sensing, and transport of NO. Alternatively, NO can be generated from nitrite by heme- and copper-containing nitrite reductases (NIRs). The NO-bearing small molecules such as nitrosothiols and dinitrosyl iron complexes (DNICs) can serve as an alternative vehicle for NO storage and transport. Once NO is formed, the rich reaction chemistry of NO leads to a wide variety of biological activities including reduction of NO by heme or non-heme iron-containing NO reductases and protein post-translational modifications by DNICs. Much of our understanding of the reactivity of metal sites in biology with NO and the mechanisms of these transformations has come from the elucidation of the geometric and electronic structures and chemical reactivity of synthetic model systems, in synergy with biochemical and biophysical studies on the relevant proteins themselves. This review focuses on recent advancements from studies on proteins and model complexes that not only have improved our understanding of the biological roles of NO but also have provided foundations for biomedical research and for bio-inspired catalyst design in energy science.
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Affiliation(s)
- Nicolai Lehnert
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Eunsuk Kim
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - Hai T Dong
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Jill B Harland
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Andrew P Hunt
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Elizabeth C Manickas
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Kady M Oakley
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - John Pham
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - Garrett C Reed
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Victor Sosa Alfaro
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
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5
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Rabe P, Kamps JJAG, Sutherlin KD, Linyard JDS, Aller P, Pham CC, Makita H, Clifton I, McDonough MA, Leissing TM, Shutin D, Lang PA, Butryn A, Brem J, Gul S, Fuller FD, Kim IS, Cheah MH, Fransson T, Bhowmick A, Young ID, O'Riordan L, Brewster AS, Pettinati I, Doyle M, Joti Y, Owada S, Tono K, Batyuk A, Hunter MS, Alonso-Mori R, Bergmann U, Owen RL, Sauter NK, Claridge TDW, Robinson CV, Yachandra VK, Yano J, Kern JF, Orville AM, Schofield CJ. X-ray free-electron laser studies reveal correlated motion during isopenicillin N synthase catalysis. SCIENCE ADVANCES 2021; 7:eabh0250. [PMID: 34417180 PMCID: PMC8378823 DOI: 10.1126/sciadv.abh0250] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 06/29/2021] [Indexed: 05/23/2023]
Abstract
Isopenicillin N synthase (IPNS) catalyzes the unique reaction of l-δ-(α-aminoadipoyl)-l-cysteinyl-d-valine (ACV) with dioxygen giving isopenicillin N (IPN), the precursor of all natural penicillins and cephalosporins. X-ray free-electron laser studies including time-resolved crystallography and emission spectroscopy reveal how reaction of IPNS:Fe(II):ACV with dioxygen to yield an Fe(III) superoxide causes differences in active site volume and unexpected conformational changes that propagate to structurally remote regions. Combined with solution studies, the results reveal the importance of protein dynamics in regulating intermediate conformations during conversion of ACV to IPN. The results have implications for catalysis by multiple IPNS-related oxygenases, including those involved in the human hypoxic response, and highlight the power of serial femtosecond crystallography to provide insight into long-range enzyme dynamics during reactions presently impossible for nonprotein catalysts.
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Affiliation(s)
- Patrick Rabe
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Jos J A G Kamps
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
- Diamond Light Source, Diamond House, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, Oxfordshire OX11 0FA, UK
| | - Kyle D Sutherlin
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - James D S Linyard
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Pierre Aller
- Diamond Light Source, Diamond House, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, Oxfordshire OX11 0FA, UK
| | - Cindy C Pham
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Hiroki Makita
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Ian Clifton
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Michael A McDonough
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Thomas M Leissing
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Denis Shutin
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Pauline A Lang
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Agata Butryn
- Diamond Light Source, Diamond House, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, Oxfordshire OX11 0FA, UK
| | - Jürgen Brem
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Sheraz Gul
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Franklin D Fuller
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - In-Sik Kim
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Mun Hon Cheah
- Department of Chemistry - Ångström, Molecular Biomimetics, Uppsala University, SE 751 20 Uppsala, Sweden
| | - Thomas Fransson
- Interdisciplinary Center for Scientific Computing, University of Heidelberg, 69120 Heidelberg, Germany
| | - Asmit Bhowmick
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Iris D Young
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, 600 16th Street, San Francisco, CA 94158, USA
| | - Lee O'Riordan
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Aaron S Brewster
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Ilaria Pettinati
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Margaret Doyle
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Yasumasa Joti
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Shigeki Owada
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Kensuke Tono
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Alexander Batyuk
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Mark S Hunter
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Roberto Alonso-Mori
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Uwe Bergmann
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
- Department of Physics, University of Wisconsin-Madison, 1150 University Avenue, Madison, WI 53706, USA
| | - Robin L Owen
- Diamond Light Source, Diamond House, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - Nicholas K Sauter
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Timothy D W Claridge
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Carol V Robinson
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Vittal K Yachandra
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Junko Yano
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Jan F Kern
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA.
| | - Allen M Orville
- Diamond Light Source, Diamond House, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK.
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, Oxfordshire OX11 0FA, UK
| | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK.
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6
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Brandis JEP, Kihn KC, Taraban MB, Schnorr J, Confer AM, Batelu S, Sun D, Rodriguez JD, Jiang W, Goldberg DP, Langguth P, Stemmler TL, Yu YB, Kane MA, Polli JE, Michel SLJ. Evaluation of the Physicochemical Properties of the Iron Nanoparticle Drug Products: Brand and Generic Sodium Ferric Gluconate. Mol Pharm 2021; 18:1544-1557. [PMID: 33621099 DOI: 10.1021/acs.molpharmaceut.0c00922] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Complex iron nanoparticle-based drugs are one of the oldest and most frequently administered classes of nanomedicines. In the US, there are seven FDA-approved iron nanoparticle reference drug products, of which one also has an approved generic drug product (i.e., sodium ferric gluconate (SFG)). These products are indicated for the treatment of iron deficiency anemia and are administered intravenously. On the molecular level, iron nanomedicines are colloids composed of an iron oxide core with a carbohydrate coating. This formulation makes nanomedicines more complex than conventional small molecule drugs. As such, these products are often referred to as nonbiological complex drugs (e.g., by the nonbiological complex drugs (NBCD) working group) or complex drug products (e.g., by the FDA). Herein, we report a comprehensive study of the physiochemical properties of the iron nanoparticle product SFG. SFG is the single drug for which both an innovator (Ferrlecit) and generic product are available in the US, allowing for comparative studies to be performed. Measurements focused on the iron core of SFG included optical spectroscopy, inductively coupled plasma mass spectrometry (ICP-MS), X-ray powder diffraction (XRPD), 57Fe Mössbauer spectroscopy, and X-ray absorbance spectroscopy (XAS). The analysis revealed similar ferric-iron-oxide structures. Measurements focused on the carbohydrate shell comprised of the gluconate ligands included forced acid degradation, dynamic light scattering (DLS), analytical ultracentrifugation (AUC), and gel permeation chromatography (GPC). Such analysis revealed differences in composition for the innovator versus the generic SFG. These studies have the potential to contribute to future quality assessment of iron complex products and will inform on a pharmacokinetic study of two therapeutically equivalent iron gluconate products.
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Affiliation(s)
- Joel E P Brandis
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201, United States
| | - Kyle C Kihn
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201, United States
| | - Marc B Taraban
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201, United States
| | - Julia Schnorr
- Department of Pharmaceutical Technology and Biopharmaceutics, Johannes Gutenberg University Mainz, Staudingerweg 5, 55128 Mainz, Germany
| | - Alex M Confer
- Department of Chemistry, The Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Sharon Batelu
- Department of Pharmaceutical Sciences, Wayne State University, Detroit, Michigan 48201, United States
| | - Dajun Sun
- Office of Research and Standards, Office of Generic Drugs, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland 20993, United States
| | - Jason D Rodriguez
- Division of Pharmaceutical Analysis, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, St. Louis, MO 20903, United States
| | - Wenlei Jiang
- Office of Research and Standards, Office of Generic Drugs, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland 20993, United States
| | - David P Goldberg
- Department of Chemistry, The Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Peter Langguth
- Department of Pharmaceutical Technology and Biopharmaceutics, Johannes Gutenberg University Mainz, Staudingerweg 5, 55128 Mainz, Germany
| | - Timothy L Stemmler
- Department of Pharmaceutical Sciences, Wayne State University, Detroit, Michigan 48201, United States
| | - Yihua Bruce Yu
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201, United States
| | - Maureen A Kane
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201, United States
| | - James E Polli
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201, United States
| | - Sarah L J Michel
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201, United States
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7
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Ould Hamouda A, Dutin F, Degert J, Tondusson M, Naim A, Rosa P, Freysz E. Study of the Photoswitching of a Fe(II) Chiral Complex through Linear and Nonlinear Ultrafast Spectroscopy. J Phys Chem Lett 2019; 10:5975-5982. [PMID: 31536709 DOI: 10.1021/acs.jpclett.9b01946] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Photoswitching the physical properties of molecular systems opens large possibilities for driving materials far from equilibrium toward new states. Moreover, ultrashort pulses of light make it possible to induce and to record photoswitching on a very short time scale, opening the way to fascinating new functionalities. Among molecular materials, Fe(II) complexes exhibit an ultrafast spin-state transition during which the spin state of the complex switches from a low spin state (LS, S = 0) to a high spin state (HS, S = 2). The latter process is remarkable: It takes place within ∼100 fs with a quantum efficiency of ∼100%. Moreover, the spin-state switching induces an important shift of the broad metal-to-ligand absorption band of the complex, and it results in large modifications of the physical and chemical properties of the compounds. But because most of the Fe(II) complexes crystallize in centrosymmetric space groups, this prevents them from exhibiting piezoelectric, ferroelectric, as well as second-order nonlinear optical properties such as second-harmonic generation (SHG). This considerably limits their potential applications. We have recently synthesized [Fe(phen)3] [Δ-As2(tartrate)2] chiral complexes that crystallize in a noncentrosymmetric 32 space group. Hereafter, upon the excitation of a thin film of these complexes by a femtosecond laser pulse and performing simultaneously transient absorption (TRA) and time-resolved SHG (TRSH) measurements, we have recorded the ultrafast LS to HS switching. Whereas a single TRA measurement gives only partial information, we demonstrate that TRSH readily reveals the different mechanisms in play during the HS-to-LS state relaxation. Moreover, a simple model makes it possible to evaluate the relaxation times as well as the hyperpolarizabilities of the different excited states through which the system travels during the spin-state transition.
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Affiliation(s)
- Amine Ould Hamouda
- CNRS, Univ. Bordeaux, LOMA UMR 5798 , 351 Cours de la Libération , 33405 Talence , France
| | - Frédéric Dutin
- CNRS, Univ. Bordeaux, LOMA UMR 5798 , 351 Cours de la Libération , 33405 Talence , France
| | - Jérôme Degert
- CNRS, Univ. Bordeaux, LOMA UMR 5798 , 351 Cours de la Libération , 33405 Talence , France
| | - Marc Tondusson
- CNRS, Univ. Bordeaux, LOMA UMR 5798 , 351 Cours de la Libération , 33405 Talence , France
| | - Ahmad Naim
- CNRS, Univ. Bordeaux, Bordeaux INP, ICMCB, UMR 5026 , F-33600 Pessac , France
| | - Patrick Rosa
- CNRS, Univ. Bordeaux, Bordeaux INP, ICMCB, UMR 5026 , F-33600 Pessac , France
| | - Eric Freysz
- CNRS, Univ. Bordeaux, LOMA UMR 5798 , 351 Cours de la Libération , 33405 Talence , France
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8
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Banerjee A, Li J, Speelman AL, White CJ, Pawlak PL, Brennessel WW, Lehnert N, Chavez FA. A Structural Model for the Iron-Nitrosyl Adduct of Gentisate Dioxygenase. Eur J Inorg Chem 2018; 2018:4797-4804. [PMID: 32577096 DOI: 10.1002/ejic.201800992] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
We present the synthesis, properties, and characterization of [Fe(T1Et4iPrIP)(NO)(H2O)2](OTf)2 (1) (T1Et4iPrIP = Tris(1-ethyl-4-isopropyl-imidazolyl)phosphine) as a model for the nitrosyl adduct of gentisate 1,2-dioxygenase (GDO). The further characterization of [Fe(T1Et4iPrIP)(THF)(NO)(OTf)](OTf) (2) which was previously communicated (Inorg. Chem. 2014, 53, 5414) is also presented. The weighted average Fe-N-O angle of 162° for 1 is very close to linear (≥ 165°) for these types of complexes. The coordinated water ligands participate in hydrogen bonding interactions. The spectral properties (EPR, UV-vis, FTIR) for 1 are compared with 2 and found to be quite comparable. Complex 1 closely follows the relationship between the Fe-N-O angle and NO vibrational frequency which was previously identified for 6-coordinate {FeNO}7 complexes. Liquid FTIR studies on 2 indicate that the ν(NO) vibration position is sensitive to solvent shifting to lower energy (relative to the solid) in donor solvent THF and shifting to higher energy in dichloromethane. The basis for this behavior is discussed. The K eq for NO binding in 2 was calculated in THF and found to be 470 M-1. Density functional theory (DFT) studies on 1 indicate donation of electron density to the iron center from the π* orbitals of formally NO-. Such a donation accounts for the near linearity of the Fe-N-O bond and the large ν(NO) value of 1791 cm-1.
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Affiliation(s)
- Atanu Banerjee
- Department of Chemistry, Oakland University, Rochester, MI 48309-4477, USA
| | - Jia Li
- Department of Chemistry, Oakland University, Rochester, MI 48309-4477, USA
| | - Amy L Speelman
- Department of Chemistry, The University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Corey J White
- Department of Chemistry, The University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Piotr L Pawlak
- Department of Chemistry, Oakland University, Rochester, MI 48309-4477, USA
| | | | - Nicolai Lehnert
- Department of Chemistry, The University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Ferman A Chavez
- Department of Chemistry, Oakland University, Rochester, MI 48309-4477, USA
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9
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Dzul SP, Rocha AG, Rawat S, Kandegedara A, Kusowski A, Pain J, Murari A, Pain D, Dancis A, Stemmler TL. In vitro characterization of a novel Isu homologue from Drosophila melanogaster for de novo FeS-cluster formation. Metallomics 2017; 9:48-60. [PMID: 27738674 DOI: 10.1039/c6mt00163g] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
FeS-clusters are utilized by numerous proteins within several biological pathways that are essential for life. In eukaryotes, the primary FeS-cluster production pathway is the mitochondrial iron-sulfur cluster (ISC) pathway. In Saccharomyces cerevisiae, de novo FeS-cluster formation is accomplished through coordinated assembly with the substrates iron and sulfur by the scaffold assembly protein "Isu1". Sulfur for cluster assembly is provided by cysteine desulfurase "Nfs1", a protein that works in union with its accessory protein "Isd11". Frataxin "Yfh1" helps direct cluster assembly by serving as a modulator of Nfs1 activity, by assisting in the delivery of sulfur and Fe(ii) to Isu1, or more likely through a combination of these and other possible roles. In vitro studies on the yeast ISC machinery have been limited, however, due to the inherent instability of recombinant Isu1. Isu1 is a molecule prone to degradation and aggregation. To circumvent Isu1 instability, we have replaced yeast Isu1 with the fly ortholog to stabilize our in vitro ISC assembly system and assist us in elucidating molecular details of the yeast ISC pathway. Our laboratory previously observed that recombinant frataxin from Drosophila melanogaster has remarkable stability compared to the yeast ortholog. Here we provide the first characterization of D. melanogaster Isu1 (fIscU) and demonstrate its ability to function within the yeast ISC machinery both in vivo and in vitro. Recombinant fIscU has physical properties similar to that of yeast Isu1. It functions as a stable dimer with similar Fe(ii) affinity and ability to form two 2Fe-2S clusters as the yeast dimer. The fIscU and yeast ISC proteins are compatible in vitro; addition of Yfh1 to Nfs1-Isd11 increases the rate of FeS-cluster formation on fIscU to a similar extent observed with Isu1. Finally, fIscU expressed in mitochondria of a yeast strain lacking Isu1 (and its paralog Isu2) is able to completely reverse the deletion phenotypes. These results demonstrate fIscU can functionally replace yeast Isu1 and it can serve as a powerful tool for exploring molecular details within the yeast ISC pathway.
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Affiliation(s)
- Stephen P Dzul
- Departments of Pharmaceutical Science, and Biochemistry and Molecular Biology, Wayne State University, Detroit, MI 48201, USA
| | - Agostinho G Rocha
- Department of Medicine, Division of Hematology-Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Swati Rawat
- Departments of Pharmaceutical Science, and Biochemistry and Molecular Biology, Wayne State University, Detroit, MI 48201, USA
| | - Ashoka Kandegedara
- Departments of Pharmaceutical Science, and Biochemistry and Molecular Biology, Wayne State University, Detroit, MI 48201, USA
| | - April Kusowski
- Departments of Pharmaceutical Science, and Biochemistry and Molecular Biology, Wayne State University, Detroit, MI 48201, USA
| | - Jayashree Pain
- Department of Pharmacology, Physiology, and Neuroscience, New Jersey Medical School, Rutgers University, Newark, New Jersey 07103, USA
| | - Anjaneyulu Murari
- Department of Pharmacology, Physiology, and Neuroscience, New Jersey Medical School, Rutgers University, Newark, New Jersey 07103, USA
| | - Debkumar Pain
- Department of Pharmacology, Physiology, and Neuroscience, New Jersey Medical School, Rutgers University, Newark, New Jersey 07103, USA
| | - Andrew Dancis
- Department of Medicine, Division of Hematology-Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Timothy L Stemmler
- Departments of Pharmaceutical Science, and Biochemistry and Molecular Biology, Wayne State University, Detroit, MI 48201, USA
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10
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Wolf M, Klüfers P. Structure and Bonding of High‐Spin Nitrosyl–Iron(II) Compounds with Mixed N,O‐Chelators and Aqua Ligands. Eur J Inorg Chem 2017. [DOI: 10.1002/ejic.201601329] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Markus Wolf
- Department Chemie Ludwig‐Maximilians‐Universität München Butenandtstraße 5‐13 82377 München Germany
| | - Peter Klüfers
- Department Chemie Ludwig‐Maximilians‐Universität München Butenandtstraße 5‐13 82377 München Germany
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11
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Aas BM, Klüfers P. The Structural Chemistry of Stable High‐Spin Nitrosyl–Iron(II) Compounds with Aminecarboxylato Co‐Ligands in Aqueous Solution. Eur J Inorg Chem 2017. [DOI: 10.1002/ejic.201601330] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Bianca M. Aas
- Department Chemie Ludwig‐Maximilians‐Universität München Butenandtstraße 5‐13 82377 München Germany
| | - Peter Klüfers
- Department Chemie Ludwig‐Maximilians‐Universität München Butenandtstraße 5‐13 82377 München Germany
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12
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Li J, Banerjee A, Pawlak PL, Brennessel WW, Chavez FA. Highest Recorded N–O Stretching Frequency for 6-Coordinate {Fe-NO}7 Complexes: An Iron Nitrosyl Model for His3 Active Sites. Inorg Chem 2014; 53:5414-6. [DOI: 10.1021/ic500558j] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Jia Li
- Department of Chemistry, Oakland University, Rochester, Michigan 48309-4477, United States
| | - Atanu Banerjee
- Department of Chemistry, Oakland University, Rochester, Michigan 48309-4477, United States
| | - Piotr L. Pawlak
- Department of Chemistry, Oakland University, Rochester, Michigan 48309-4477, United States
| | - William W. Brennessel
- Department of Chemistry, University of Rochester, Rochester, New York 14627-0216, United States
| | - Ferman A. Chavez
- Department of Chemistry, Oakland University, Rochester, Michigan 48309-4477, United States
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13
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Clifton IJ, Ge W, Adlington RM, Baldwin JE, Rutledge PJ. The crystal structure of an isopenicillin N synthase complex with an ethereal substrate analogue reveals water in the oxygen binding site. FEBS Lett 2013; 587:2705-9. [DOI: 10.1016/j.febslet.2013.07.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Revised: 07/04/2013] [Accepted: 07/04/2013] [Indexed: 10/26/2022]
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14
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Hamed RB, Gomez-Castellanos JR, Henry L, Ducho C, McDonough MA, Schofield CJ. The enzymes of β-lactam biosynthesis. Nat Prod Rep 2013; 30:21-107. [DOI: 10.1039/c2np20065a] [Citation(s) in RCA: 146] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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15
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Berto TC, Speelman AL, Zheng S, Lehnert N. Mono- and dinuclear non-heme iron–nitrosyl complexes: Models for key intermediates in bacterial nitric oxide reductases. Coord Chem Rev 2013. [DOI: 10.1016/j.ccr.2012.05.007] [Citation(s) in RCA: 144] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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16
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Mijovilovich A, Hayashi H, Kawamura N, Osawa H, Bruijnincx PCA, Klein Gebbink RJM, de Groot FMF, Weckhuysen BM. Kβ Detected High-Resolution XANES of FeII and FeIII Models of the 2-His-1-Carboxylate Motif: Analysis of the Carboxylate Binding Mode. Eur J Inorg Chem 2012. [DOI: 10.1002/ejic.201101075] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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17
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Brown-Marshall CD, Diebold AR, Solomon EI. Reaction coordinate of isopenicillin N synthase: oxidase versus oxygenase activity. Biochemistry 2010; 49:1176-82. [PMID: 20078029 DOI: 10.1021/bi901772w] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Isopenicillin N synthase (IPNS) can have both oxidase and oxygenase activity depending on the substrate. For the native substrate, ACV, oxidase activity exists; however, for the substrate analogue ACOV, which lacks an amide nitrogen, IPNS exhibits oxygenase activity. The potential energy surfaces for the O-O bond elongation and cleavage were calculated for three different reactions: homolytic cleavage via traditional Fenton chemistry, heterolytic cleavage, and nucleophilic attack. These surfaces show that the hydroperoxide-ferrous intermediate, formed by O(2)-activated H atom abstraction from the substrate, can exploit different reaction pathways and that interactions with the substrate govern the pathway. The hydrogen bonds from hydroperoxide to the amide nitrogen of ACV polarize the sigma* orbital of the peroxide toward the proximal oxygen, facilitating heterolytic cleavage. For the substrate analogue ACOV, this hydrogen bond is no longer present, leading to nucleophilic attack on the substrate intermediate C-S bond. After cleavage of the hydroperoxide, the two reaction pathways proceed with minimal barriers, resulting in the closure of the beta-lactam ring for the oxidase activity (ACV) or formation of the thiocarboxylate for oxygenase activity (ACOV).
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18
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Salomone-Stagni M, Stellato F, Whaley CM, Vogt S, Morante S, Shima S, Rauchfuss TB, Meyer-Klaucke W. The iron-site structure of [Fe]-hydrogenase and model systems: an X-ray absorption near edge spectroscopy study. Dalton Trans 2010; 39:3057-64. [PMID: 20221540 PMCID: PMC3465567 DOI: 10.1039/b922557a] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The [Fe]-hydrogenase is an ideal system for studying the electronic properties of the low spin iron site that is common to the catalytic centres of all hydrogenases. Because they have no auxiliary iron-sulfur clusters and possess a cofactor containing a single iron centre, the [Fe]-hydrogenases are well suited for spectroscopic analysis of those factors required for the activation of molecular hydrogen. Specifically, in this study we shed light on the electronic and molecular structure of the iron centre by XAS analysis of [Fe]-hydrogenase from Methanocaldococcus jannashii and five model complexes (Fe(ethanedithiolate)(CO)(2)(PMe(3))(2), [K(18-crown-6)](2)[Fe(CN)(2)(CO)(3)], K[Fe(CN)(CO)(4)], K(3)[Fe(III)(CN)(6)], K(4)[Fe(II)(CN)(6)]). The different electron donors have a strong influence on the iron absorption K-edge energy position, which is frequently used to determine the metal oxidation state. Our results demonstrate that the K-edges of Fe(II) complexes, achieved with low-spin ferrous thiolates, are consistent with a ferrous centre in the [Fe]-hydrogenase from Methanocaldococcus jannashii. The metal geometry also strongly influences the XANES and thus the electronic structure. Using in silico simulation, we were able to reproduce the main features of the XANES spectra and describe the effects of individual donor contributions on the spectra. Thereby, we reveal the essential role of an unusual carbon donor coming from an acyl group of the cofactor in the determination of the electronic structure required for the activity of the enzyme.
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Affiliation(s)
| | - Francesco Stellato
- Physics Department and INFN, Università di Roma “Tor Vergata”, Via della ricerca scientifica 1, I-00133, Roma, Italy
| | - C. Matthew Whaley
- Department of Chemistry, University of Illinois, A328 Chemical & Life Science Lab, 600 South Mathews Avenue, IL-61801, Urbana, USA
| | - Sonja Vogt
- Max-Planck-Institute für terrestrische Mikrobiologie, Karl-von-Frisch-Straβe, D-35043, Marburg, Germany
| | - Silvia Morante
- Physics Department and INFN, Università di Roma “Tor Vergata”, Via della ricerca scientifica 1, I-00133, Roma, Italy
| | - Seigo Shima
- Max-Planck-Institute für terrestrische Mikrobiologie, Karl-von-Frisch-Straβe, D-35043, Marburg, Germany
| | - Thomas B. Rauchfuss
- Department of Chemistry, University of Illinois, A328 Chemical & Life Science Lab, 600 South Mathews Avenue, IL-61801, Urbana, USA
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19
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Mijovilovich A. XANES Study of the Carboxylate Binding Mode in Two Pterin Hydroxylases. Chem Biodivers 2008; 5:2131-2139. [DOI: 10.1002/cbdv.200890194] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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20
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Comparative Fe and Zn K-edge X-ray absorption spectroscopic study of the ferroxidase centres of human H-chain ferritin and bacterioferritin from Desulfovibrio desulfuricans. J Biol Inorg Chem 2008; 14:35-49. [DOI: 10.1007/s00775-008-0422-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2008] [Accepted: 08/12/2008] [Indexed: 10/21/2022]
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21
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Chai SC, Ju T, Dang M, Goldsmith RB, Maroney MJ, Pochapsky TC. Characterization of metal binding in the active sites of acireductone dioxygenase isoforms from Klebsiella ATCC 8724. Biochemistry 2008; 47:2428-38. [PMID: 18237192 DOI: 10.1021/bi7004152] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The two acireductone dioxygenase (ARD) isozymes from the methionine salvage pathway of Klebsiella ATCC 8724 present an unusual case in which two enzymes with different structures and distinct activities toward their common substrates (1,2-dihydroxy-3-oxo-5-(methylthio)pent-1-ene and dioxygen) are derived from the same polypeptide chain. Structural and functional differences between the two isozymes are determined by the type of M2+ metal ion bound in the active site. The Ni2+-bound NiARD catalyzes an off-pathway shunt from the methionine salvage pathway leading to the production of formate, methylthiopropionate, and carbon monoxide, while the Fe2+-bound FeARD' catalyzes the on-pathway formation of methionine precursor 2-keto-4-methylthiobutyrate and formate. Four potential protein-based metal ligands were identified by sequence homology and structural considerations. Based on the results of site-directed mutagenesis experiments, X-ray absorption spectroscopy (XAS), and isothermal calorimetry measurements, it is concluded that the same four residues, His96, His98, Glu102 and His140, provide the protein-based ligands for the metal in both the Ni- and Fe-containing forms of the enzyme, and subtle differences in the local backbone conformations trigger the observed structural and functional differences between the FeARD' and NiARD isozymes. Furthermore, both forms of the enzyme bind their respective metals with pseudo-octahedral geometry, and both may lose a histidine ligand upon binding of substrate under anaerobic conditions. However, mutations at two conserved nonligand acidic residues, Glu95 and Glu100, result in low metal contents for the mutant proteins as isolated, suggesting that some of the conserved charged residues may aid in transfer of metal from in vivo sources or prevent the loss of metal to stronger chelators. The Glu100 mutant reconstitutes readily but has low activity. Mutation of Asp101 results in an active enzyme that incorporates metal in vivo but shows evidence of mixed forms.
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Affiliation(s)
- Sergio C Chai
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, USA
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22
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Stewart AC, Clifton IJ, Adlington RM, Baldwin JE, Rutledge PJ. A Cyclobutanone Analogue Mimics Penicillin in Binding to Isopenicillin N Synthase. Chembiochem 2007; 8:2003-7. [PMID: 17907118 DOI: 10.1002/cbic.200700176] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
A carbocyclic analogue of the beta-lactam antibiotic isopenicillin N (IPN) has been synthesised and cocrystallised with isopenicillin N synthase (IPNS), the central enzyme in the biosynthesis of penicillin antibiotics. The crystal structure of the IPNS-cyclobutanone complex reveals an active site environment similar to that seen in the enzyme-product complex generated by turnover of the natural substrate within the crystalline protein. The IPNS-cyclobutanone structure demonstrates that the product analogue is tethered to the protein by hydrogen bonding and salt bridge interactions with its carboxylate groups, as seen previously for the natural substrate and product. Furthermore, the successful cocrystallisation of this analogue with IPNS provides firm structural evidence for the utility of such cyclobutanone derivatives as hydrolytically stable analogues of bicyclic beta-lactams.
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Affiliation(s)
- Amanda C Stewart
- Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
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23
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Brown CD, Neidig ML, Neibergall MB, Lipscomb JD, Solomon EI. VTVH-MCD and DFT studies of thiolate bonding to [FeNO]7/[FeO2]8 complexes of isopenicillin N synthase: substrate determination of oxidase versus oxygenase activity in nonheme Fe enzymes. J Am Chem Soc 2007; 129:7427-38. [PMID: 17506560 PMCID: PMC2536647 DOI: 10.1021/ja071364v] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Isopenicillin N synthase (IPNS) is a unique mononuclear nonheme Fe enzyme that catalyzes the four-electron oxidative double ring closure of its substrate ACV. A combination of spectroscopic techniques including EPR, absorbance, circular dichroism (CD), magnetic CD, and variable-temperature, variable-field MCD (VTVH-MCD) were used to evaluate the geometric and electronic structure of the [FeNO]7 complex of IPNS coordinated with the ACV thiolate ligand. Density Function Theory (DFT) calculations correlated to the spectroscopic data were used to generate an experimentally calibrated bonding description of the Fe-IPNS-ACV-NO complex. New spectroscopic features introduced by the binding of the ACV thiolate at 13 100 and 19 800 cm-1 are assigned as the NO pi*(ip) --> Fe dx2-y2 and S pi--> Fe dx2-y2 charge transfer (CT) transitions, respectively. Configuration interaction mixes S CT character into the NO pi*(ip) --> Fe dx2-y2 CT transition, which is observed experimentally from the VTVH-MCD data from this transition. Calculations on the hypothetical {FeO2}8 complex of Fe-IPNS-ACV reveal that the configuration interaction present in the [FeNO]7 complex results in an unoccupied frontier molecular orbital (FMO) with correct orientation and distal O character for H-atom abstraction from the ACV substrate. The energetics of NO/O2 binding to Fe-IPNS-ACV were evaluated and demonstrate that charge donation from the ACV thiolate ligand renders the formation of the FeIII-superoxide complex energetically favorable, driving the reaction at the Fe center. This single center reaction allows IPNS to avoid the O2 bridged binding generally invoked in other nonheme Fe enzymes that leads to oxygen insertion (i.e., oxygenase function) and determines the oxidase activity of IPNS.
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Affiliation(s)
- Christina D Brown
- Department of Chemistry, Stanford University, Stanford, California 94305-5080, USA
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24
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Ju T, Goldsmith RB, Chai SC, Maroney MJ, Pochapsky SS, Pochapsky TC. One protein, two enzymes revisited: a structural entropy switch interconverts the two isoforms of acireductone dioxygenase. J Mol Biol 2006; 363:823-34. [PMID: 16989860 PMCID: PMC1808343 DOI: 10.1016/j.jmb.2006.08.060] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2006] [Revised: 08/22/2006] [Accepted: 08/23/2006] [Indexed: 12/01/2022]
Abstract
Acireductone dioxygenase (ARD) catalyzes different reactions between O2 and 1,2-dihydroxy-3-oxo-5-(methylthio)pent-1-ene (acireductone) depending upon the metal bound in the active site. Ni2+ -ARD cleaves acireductone to formate, CO and methylthiopropionate. If Fe2+ is bound (ARD'), the same substrates yield methylthioketobutyrate and formate. The two forms differ in structure, and are chromatographically separable. Paramagnetism of Fe2+ renders the active site of ARD' inaccessible to standard NMR methods. The structure of ARD' has been determined using Fe2+ binding parameters determined by X-ray absorption spectroscopy and NMR restraints from H98S ARD, a metal-free diamagnetic protein that is isostructural with ARD'. ARD' retains the beta-sandwich fold of ARD, but a structural entropy switch increases order at one end of a two-helix system that bisects the beta-sandwich and decreases order at the other upon interconversion of ARD and ARD', causing loss of the C-terminal helix in ARD' and rearrangements of residues involved in substrate orientation in the active site.
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Affiliation(s)
- Tingting Ju
- Department of Chemistry, Brandeis University MS 015, 415 South St., Waltham, MA 02454-9110 USA
| | | | - Sergio C. Chai
- Department of Chemistry, University of Massachusetts Amherst, MA 01003-9336 USA
| | - Michael J. Maroney
- Department of Chemistry, University of Massachusetts Amherst, MA 01003-9336 USA
| | - Susan Sondej Pochapsky
- Department of Chemistry, Brandeis University MS 015, 415 South St., Waltham, MA 02454-9110 USA
| | - Thomas C. Pochapsky
- Department of Chemistry, Brandeis University MS 015, 415 South St., Waltham, MA 02454-9110 USA
- Department of Biochemistry, Brandeis University
- Rosensteil Basic Medical Sciences Institute, Brandeis University
- Correspondence should be addressed to TCP: Phone 781-736-2559, Fax 781-736-2516 , Website http://www.chem.brandeis.edu/pochapsky
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Daruzzaman A, Clifton IJ, Adlington RM, Baldwin JE, Rutledge PJ. Unexpected Oxidation of a Depsipeptide Substrate Analogue in Crystalline Isopenicillin N Synthase. Chembiochem 2006; 7:351-8. [PMID: 16444759 DOI: 10.1002/cbic.200500282] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Isopenicillin N synthase (IPNS) is a non-heme iron(ii)-dependent oxidase that is central to penicillin biosynthesis. Herein, we report mechanistic studies of the IPNS reaction in the crystalline state, using the substrate analogue delta-(L-alpha-aminoadipoyl)-(3R)-methyl-L-cysteine D-alpha-hydroxyisovaleryl ester (AmCOV) to probe the early stages of the catalytic cycle. The X-ray crystal structure of the anaerobic IPNS:Fe(II):AmCOV complex was solved to 1.40 A resolution, and it reveals several subtle differences in the active site relative to the complex of the enzyme with its natural substrate. The crystalline IPNS:Fe(II):AmCOV complex was then exposed to oxygen gas at high pressure; this brought about reaction to give what appears to be a hydroxymethyl/ene-thiol product. A mechanism for this reaction is proposed. These results offer further insight into the delicate interplay of steric and electronic effects in the IPNS active site and the mechanistic intricacies of this remarkable enzyme.
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Affiliation(s)
- Adam Daruzzaman
- Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
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26
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Wasser IM, Huang HW, Moënne-Loccoz P, Karlin KD. Heme/non-heme diiron(II) complexes and O2, CO, and NO adducts as reduced and substrate-bound models for the active site of bacterial nitric oxide reductase. J Am Chem Soc 2005; 127:3310-20. [PMID: 15755147 DOI: 10.1021/ja0458773] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
As a first generation model for the reactive reduced active-site form of bacterial nitric oxide reductase, a heme/non-heme diiron(II) complex [(6L)Fe(II)...Fe(II)-(Cl)]+ (2) {where 6L = partially fluorinated tetraphenylporphyrin with a tethered tetradentate TMPA chelate; TMPA = tris(2-pyridyl)amine} was generated by reduction of the corresponding mu-oxo diferric compound [(6L)Fe(III)-O-Fe(III)-Cl]+ (1). Coordination chemistry models for reactions of reduced NOR with O2, CO, and NO were also developed. With O2 and CO, adducts are formed, [(6L)Fe(III)(O2-))(thf)...Fe(II)-Cl]B(C6F5)4 (2a x O2) {lambda(max) 418 (Soret), 536 nm; nu(O-O) = 1176 cm(-1), nu(Fe-O) = 574 cm(-1) and [(6L)Fe(II)(CO)(thf)Fe(II)-Cl]B(C6F5)4 (2a x CO) {nu(CO) 1969 cm(-1)}, respectively. Reaction of purified nitric oxide with 2 leads to the dinitrosyl complex [(6L)Fe(NO)Fe(NO)-Cl]B(C6F5)4 (2a x (NO)2) with nu(NO) absorptions at 1798 cm(-1) (non-heme Fe-NO) and 1689 cm(-1) (heme-NO).
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Affiliation(s)
- Ian M Wasser
- Department of Chemistry, Johns Hopkins University, Charles and 34 Streets, Baltimore, Maryland 21218, USA
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Breece RM, Costello A, Bennett B, Sigdel TK, Matthews ML, Tierney DL, Crowder MW. A Five-coordinate Metal Center in Co(II)-substituted VanX. J Biol Chem 2005; 280:11074-81. [PMID: 15657055 DOI: 10.1074/jbc.m412582200] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In an effort to structurally probe the metal binding site in VanX, electronic absorption, EPR, and extended x-ray absorption fine structure (EXAFS) spectroscopic studies were conducted on Co(II)-substituted VanX. Electronic spectroscopy revealed the presence of Co(II) ligand field transitions that had molar absorptivities of approximately 100 m(-1) cm(-1), which suggests that Co(II) is five-coordinate in Co(II)-substituted VanX. Low temperature EPR spectra of Co(II)-substituted VanX were simulated using spin Hamiltonian parameters of M(S) = |+/-1/2), E/D = 0.14, g(real(x,y)) = 2.37, and g(real(z)) = 2.03. These parameters lead to the prediction that Co(II) in the enzyme is five-coordinate and that there may be at least one solvent-derived ligand. Single scattering fits of EXAFS data indicate that the metal ions in both native Zn(II)-containing and Co(II)-substituted VanX have the same coordination number and that the metal ions are coordinated by 5 nitrogen/oxygen ligands at approximately 2.0 angstroms. These data demonstrate that Co(II) (and Zn(II) from EXAFS studies) is five-coordinate in VanX in contrast to previous crystallographic studies (Bussiere, D. E., Pratt, S. D., Katz, L., Severin, J. M., Holzman, T., and Park, C. H. (1998) Mol. Cell 2, 75-84). These spectroscopic studies also demonstrate that the metal ion in Co(II)-substituted VanX when complexed with a phosphinate analog of substrate D-Ala-D-Ala is also five-coordinate.
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Affiliation(s)
- Robert M Breece
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, USA
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Neidig ML, Solomon EI. Structure–function correlations in oxygen activating non-heme iron enzymes. Chem Commun (Camb) 2005:5843-63. [PMID: 16317455 DOI: 10.1039/b510233m] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A large group of mononuclear non-heme iron enzymes exist which activate dioxygen to catalyze key biochemical transformations, including many of medical, pharmaceutical and environmental significance. These enzymes utilize high-spin Fe(II) active sites and additional reducing equivalents from cofactors or substrates to react with O2 to yield iron-oxygen intermediates competent to transform substrate to product. While Fe(II) sites have been difficult to study due to the lack of dominant spectroscopic features, a spectroscopic methodology has been developed which allows the elucidation of the geometric and electronic structures of these active sites and provides molecular level insight into the mechanisms of catalysis. This review provides a summary of this methodology with emphasis on its application to the determination of important active site structure-function correlations in mononuclear non-heme iron enzymes. These studies provide key insight into the mechanisms of oxygen activation, active site features that contribute to differences in reactivity and, combined with theoretical calculations and model studies, the nature of oxygen intermediates active in catalysis.
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Costas M, Mehn MP, Jensen MP, Que L. Dioxygen Activation at Mononuclear Nonheme Iron Active Sites: Enzymes, Models, and Intermediates. Chem Rev 2004; 104:939-86. [PMID: 14871146 DOI: 10.1021/cr020628n] [Citation(s) in RCA: 2014] [Impact Index Per Article: 100.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Miquel Costas
- Departament de Quimica, Universitat de Girona, 17071, Girona, Spain
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31
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Wasser IM, de Vries S, Moënne-Loccoz P, Schröder I, Karlin KD. Nitric oxide in biological denitrification: Fe/Cu metalloenzyme and metal complex NO(x) redox chemistry. Chem Rev 2002; 102:1201-34. [PMID: 11942794 DOI: 10.1021/cr0006627] [Citation(s) in RCA: 355] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ian M Wasser
- Department of Chemistry, The Johns Hopkins University, Charles and 34th Streets, Baltimore, MD 21218, USA
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32
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Wirstam M, Siegbahn PEM. A Mechanistic Study of Isopenicillin N Formation Using Density Functional Theory. J Am Chem Soc 2000. [DOI: 10.1021/ja001103k] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Maria Wirstam
- Contribution from the Department of Physics, Stockholm University, Box 6730, S-113 85 Stockholm, Sweden
| | - Per E. M. Siegbahn
- Contribution from the Department of Physics, Stockholm University, Box 6730, S-113 85 Stockholm, Sweden
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33
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Solomon EI, Brunold TC, Davis MI, Kemsley JN, Lee SK, Lehnert N, Neese F, Skulan AJ, Yang YS, Zhou J. Geometric and electronic structure/function correlations in non-heme iron enzymes. Chem Rev 2000; 100:235-350. [PMID: 11749238 DOI: 10.1021/cr9900275] [Citation(s) in RCA: 1351] [Impact Index Per Article: 56.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- E I Solomon
- Department of Chemistry, Stanford University, Stanford, California 94305-5080
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34
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Ray M, Golombek AP, Hendrich MP, Yap GPA, Liable-Sands LM, Rheingold AL, Borovik AS. Structure and Magnetic Properties of Trigonal Bipyramidal Iron Nitrosyl Complexes. Inorg Chem 1999. [DOI: 10.1021/ic990070a] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Manabendra Ray
- Departments of Chemistry, University of Kansas, Lawrence, Kansas 66045, Carnegie-Mellon University, Pittsburgh, Pennsylvania 15213, and University of Delaware, Newark, Delaware 19716
| | - Adina P. Golombek
- Departments of Chemistry, University of Kansas, Lawrence, Kansas 66045, Carnegie-Mellon University, Pittsburgh, Pennsylvania 15213, and University of Delaware, Newark, Delaware 19716
| | - Michael P. Hendrich
- Departments of Chemistry, University of Kansas, Lawrence, Kansas 66045, Carnegie-Mellon University, Pittsburgh, Pennsylvania 15213, and University of Delaware, Newark, Delaware 19716
| | - Glenn P. A. Yap
- Departments of Chemistry, University of Kansas, Lawrence, Kansas 66045, Carnegie-Mellon University, Pittsburgh, Pennsylvania 15213, and University of Delaware, Newark, Delaware 19716
| | - Louise M. Liable-Sands
- Departments of Chemistry, University of Kansas, Lawrence, Kansas 66045, Carnegie-Mellon University, Pittsburgh, Pennsylvania 15213, and University of Delaware, Newark, Delaware 19716
| | - Arnold, L. Rheingold
- Departments of Chemistry, University of Kansas, Lawrence, Kansas 66045, Carnegie-Mellon University, Pittsburgh, Pennsylvania 15213, and University of Delaware, Newark, Delaware 19716
| | - A. S. Borovik
- Departments of Chemistry, University of Kansas, Lawrence, Kansas 66045, Carnegie-Mellon University, Pittsburgh, Pennsylvania 15213, and University of Delaware, Newark, Delaware 19716
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35
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Lloyd MD, Lee HJ, Harlos K, Zhang ZH, Baldwin JE, Schofield CJ, Charnock JM, Garner CD, Hara T, Terwisscha van Scheltinga AC, Valegård K, Viklund JA, Hajdu J, Andersson I, Danielsson A, Bhikhabhai R. Studies on the active site of deacetoxycephalosporin C synthase. J Mol Biol 1999; 287:943-60. [PMID: 10222202 DOI: 10.1006/jmbi.1999.2594] [Citation(s) in RCA: 96] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The Fe(II) and 2-oxoglutarate-dependent dioxygenase deacetoxycephalosporin C synthase (DAOCS) from Streptomyces clavuligerus was expressed at ca 25 % of total soluble protein in Escherichia coli and purified by an efficient large-scale procedure. Purified protein catalysed the conversions of penicillins N and G to deacetoxycephems. Gel filtration and light scattering studies showed that in solution monomeric apo-DAOCS is in equilibrium with a trimeric form from which it crystallizes. DAOCS was crystallized +/-Fe(II) and/or 2-oxoglutarate using the hanging drop method. Crystals diffracted to beyond 1.3 A resolution and belonged to the R3 space group (unit cell dimensions: a=b=106.4 A, c=71.2 A; alpha=beta=90 degrees, gamma=120 degrees (in the hexagonal setting)). Despite the structure revealing that Met180 is located close to the reactive oxidizing centre of DAOCS, there was no functional difference between the wild-type and selenomethionine derivatives. X-ray absorption spectroscopic studies in solution generally supported the iron co-ordination chemistry defined by the crystal structures. The Fe K-edge positions of 7121.2 and 7121.4 eV for DAOCS alone and with 2-oxoglutarate were both consistent with the presence of Fe(II). For Fe(II) in DAOCS the best fit to the Extended X-ray Absorption Fine Structure (EXAFS) associated with the Fe K-edge was found with two His imidazolate groups at 1.96 A, three nitrogen or oxygen atoms at 2.11 A and one other light atom at 2.04 A. For the Fe(II) in the DAOCS-2-oxoglutarate complex the EXAFS spectrum was successfully interpreted by backscattering from two His residues (Fe-N at 1.99 A), a bidentate O,O-co-ordinated 2-oxoglutarate with Fe-O distances of 2.08 A, another O atom at 2.08 A and one at 2.03 A. Analysis of the X-ray crystal structural data suggests a binding mode for the penicillin N substrate and possible roles for the C terminus in stabilising the enzyme and ordering the reaction mechanism.
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Affiliation(s)
- M D Lloyd
- The Dyson Perrins Laboratory and the Oxford Centre for Molecular Sciences, South Parks Road, Oxford, OX1 3QY, UK.
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36
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Tayeh MA, Howe DL, Salleh HM, Sheflyan GY, Son JK, Woodard RW. Kinetic and mutagenic evidence for the role of histidine residues in the Lycopersicon esculentum 1-aminocyclopropane-1-carboxylic acid oxidase. JOURNAL OF PROTEIN CHEMISTRY 1999; 18:55-68. [PMID: 10071929 DOI: 10.1023/a:1020647400034] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The ACCO gene from Lycopersicon esculentum (tomato) has been cloned into the expression vector PT7-7. The highly expressed protein was recovered in the form of inclusion bodies. ACCO is inactivated by diethyl pyrocarbonate (DEPC) with a second-order rate constant of 170 M(-1) min(-1). The pH-inactivation rate data imply the involvement of an amino acid residue with a pK value of 6.05. The difference UV spectrum of the the DEPC-inactivated versus native ACCO showed a single peak at 242 nm indicating the modification of histidine residues. The inactivation was reversed by the addition of hydroxylamine to the DEPC-inactivated ACCO. Substrate/cofactor protection studies indicate that both iron and ACC bind near the active site, which contains histidine residues. Four histidines of ACCO were individually mutated to alanine and glycine. H39A is catalytically active, while H177A, H177G, H211A, H211G, H234A, and H234G are basically inactive. The results indicate that histidine residues 177, 211, and 234 may serve as ligands for the active-site iron of ACCO and/or may play some important structural or catalytic role.
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Affiliation(s)
- M A Tayeh
- Interdepartmental Program in Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor 48109-1065, USA
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37
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Abstract
The most commonly used beta-lactam antibiotics for the therapy of infectious diseases are penicillin and cephalosporin. Penicillin is produced as an end product by some fungi, most notably by Aspergillus (Emericella) nidulans and Penicillium chrysogenum. Cephalosporins are synthesized by both bacteria and fungi, e.g., by the fungus Acremonium chrysogenum (Cephalosporium acremonium). The biosynthetic pathways leading to both secondary metabolites start from the same three amino acid precursors and have the first two enzymatic reactions in common. Penicillin biosynthesis is catalyzed by three enzymes encoded by acvA (pcbAB), ipnA (pcbC), and aatA (penDE). The genes are organized into a cluster. In A. chrysogenum, in addition to acvA and ipnA, a second cluster contains the genes encoding enzymes that catalyze the reactions of the later steps of the cephalosporin pathway (cefEF and cefG). Within the last few years, several studies have indicated that the fungal beta-lactam biosynthesis genes are controlled by a complex regulatory network, e. g., by the ambient pH, carbon source, and amino acids. A comparison with the regulatory mechanisms (regulatory proteins and DNA elements) involved in the regulation of genes of primary metabolism in lower eukaryotes is thus of great interest. This has already led to the elucidation of new regulatory mechanisms. Furthermore, such investigations have contributed to the elucidation of signals leading to the production of beta-lactams and their physiological meaning for the producing fungi, and they can be expected to have a major impact on rational strain improvement programs. The knowledge of biosynthesis genes has already been used to produce new compounds.
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Affiliation(s)
- A A Brakhage
- Lehrstuhl für Mikrobiologie, Universität München, D-80638 Munich, Germany.
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38
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Briganti F, Mangani S, Pedocchi L, Scozzafava A, Golovleva LA, Jadan AP, Solyanikova IP. XAS characterization of the active sites of novel intradiol ring-cleaving dioxygenases: hydroxyquinol and chlorocatechol dioxygenases. FEBS Lett 1998; 433:58-62. [PMID: 9738933 DOI: 10.1016/s0014-5793(98)00884-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The intradiol cleaving dioxygenases hydroxyquinol 1,2-dioxygenase (HQI,20) from Nocardiodes simplex 3E, chlorocatechol 1,2-dioxygenase (CIC1,20) from Rhodococcus erythropolis ICP, and their anaerobic substrate adducts (hydroxyquinol-HQ1,20 and 4-chlorocatechol-CIC1,20) have been characterized through X-ray absorption spectroscopy. In both enzymes the iron(III) is pentacoordinated and the distance distribution inside the Fe(III) first coordination shell is close to that already found in the extensively characterized protocatechuate 3,4-dioxygenase. The coordination number and the bond lengths are not significantly affected by the substrate binding. Therefore it is confirmed that the displacement of a protein donor upon substrate binding has to be considered a general step valid for all intradiol dioxygenases.
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Affiliation(s)
- F Briganti
- Dipartimento di Chimica, Università degli Studi di Firenze, Florence, Italy
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39
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Kivirikko KI, Pihlajaniemi T. Collagen hydroxylases and the protein disulfide isomerase subunit of prolyl 4-hydroxylases. ADVANCES IN ENZYMOLOGY AND RELATED AREAS OF MOLECULAR BIOLOGY 1998; 72:325-98. [PMID: 9559057 DOI: 10.1002/9780470123188.ch9] [Citation(s) in RCA: 100] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Prolyl 4-hydroxylases catalyze the formation of 4-hydroxyproline in collagens and other proteins with an appropriate collagen-like stretch of amino acid residues. The enzyme requires Fe(II), 2-oxoglutarate, molecular oxygen, and ascorbate. This review concentrates on recent progress toward understanding the detailed mechanism of 4-hydroxylase action, including: (a) occurrence and function of the enzyme in animals; (b) general molecular properties; (c) intracellular sites of hydroxylation; (d) peptide substrates and mechanistic roles of the cosubstrates; (e) insights into the development of antifibrotic drugs; (f) studies of the enzyme's subunits and their catalytic function; and (g) mutations that lead to Ehlers-Danlos Syndrome. An account of the regulation of collagen hydroxylase activities is also provided.
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Affiliation(s)
- K I Kivirikko
- Collagen Research Unit, Biocenter, University of Oulu, Finland
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40
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Abstract
The past year has witnessed significant advances in the study of oxygen-activating nonheme iron enzymes. Thirteen crystal structures of substrate and substrate analog complexes of protocatechuate 3, 4-dioxygenase have revealed intimate details about changes at the enzyme active site during catalysis. Crystallographic data have established a 2-His-1-carboxylate facial triad as a structural motif common to a number of mononuclear nonheme iron enzymes, including isopenicillin N synthase, tyrosine hydroxylase and naphthalene dioxygenase. The first metrical data has been obtained for the high valent intermediates Q and X of methane monooxygenase and ribonucleotide reductase, respectively. The number of enzymes thought to have nonheme diiron sites has been expanded to include alkene monooxygenase from Xanthobacter strain Py2 and the membrane bound alkane hydroxylase from Pseudomonas oleovorans (AlkB). Finally, synthetic complexes have successfully mimicked chemistry performed by both mono- and dinuclear nonheme iron enzymes, such as the extradiol-cleaving catechol dioxygenases, lipoxygenase, alkane and alkene monoxygenases and fatty acid desaturases.
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Affiliation(s)
- S J Lange
- Department of Chemistry Center for Metals in Biocatalysis, University of Minnesota, 207 Pleasant Street SE, Minneapolis, MN 55455, USA
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41
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Hegg EL, Que L. The 2-His-1-carboxylate facial triad--an emerging structural motif in mononuclear non-heme iron(II) enzymes. EUROPEAN JOURNAL OF BIOCHEMISTRY 1997; 250:625-9. [PMID: 9461283 DOI: 10.1111/j.1432-1033.1997.t01-1-00625.x] [Citation(s) in RCA: 371] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
A 2-His-1-carboxylate facial triad is a common feature of the active sites in a number of mononuclear non-heme iron(II) enzymes. This structural motif was established crystallographically for five different classes of enzymes and inferred from sequence similarity for two other classes. The 2-His-1-carboxylate facial triad anchors the iron in the active site and at the same time maintains three additional cis-oriented sites. These sites can be used to bind other endogenous ligands or exogenous ligands such as substrate and/or O2, giving the metal center great flexibility to use different mechanistic strategies to perform a variety of chemical transformations.
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Affiliation(s)
- E L Hegg
- Department of Chemistry and Center for Metals in Biocatalysis, University of Minnesota, Minneapolis 55455, USA
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Schofield CJ, Baldwin JE, Byford MF, Clifton I, Hajdu J, Hensgens C, Roach P. Proteins of the penicillin biosynthesis pathway. Curr Opin Struct Biol 1997; 7:857-64. [PMID: 9434907 DOI: 10.1016/s0959-440x(97)80158-3] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Two sequential steps are common to the biosynthesis of all penicillin-derived antibiotics: the reaction of three L-amino acids to give L-delta-(alpha-aminoadipoyl)-L-cysteinyl-D-valine, and the oxidation of this tripeptide to give isopenicillin N. Recent studies on the peptide synthetase and oxidase enzymes responsible for these steps have implications for the mechanisms and structures of related enzymes involved in a range of metabolic processes.
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43
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Westre TE, Kennepohl P, DeWitt JG, Hedman B, Hodgson KO, Solomon EI. A Multiplet Analysis of Fe K-Edge 1s → 3d Pre-Edge Features of Iron Complexes. J Am Chem Soc 1997. [DOI: 10.1021/ja964352a] [Citation(s) in RCA: 1051] [Impact Index Per Article: 38.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Tami E. Westre
- Contribution from the Department of Chemistry and Stanford Synchrotron Radiation Laboratory, Stanford University, Stanford, California 94305
| | - Pierre Kennepohl
- Contribution from the Department of Chemistry and Stanford Synchrotron Radiation Laboratory, Stanford University, Stanford, California 94305
| | - Jane G. DeWitt
- Contribution from the Department of Chemistry and Stanford Synchrotron Radiation Laboratory, Stanford University, Stanford, California 94305
| | - Britt Hedman
- Contribution from the Department of Chemistry and Stanford Synchrotron Radiation Laboratory, Stanford University, Stanford, California 94305
| | - Keith O. Hodgson
- Contribution from the Department of Chemistry and Stanford Synchrotron Radiation Laboratory, Stanford University, Stanford, California 94305
| | - Edward I. Solomon
- Contribution from the Department of Chemistry and Stanford Synchrotron Radiation Laboratory, Stanford University, Stanford, California 94305
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Roach PL, Clifton IJ, Hensgens CM, Shibata N, Schofield CJ, Hajdu J, Baldwin JE. Structure of isopenicillin N synthase complexed with substrate and the mechanism of penicillin formation. Nature 1997; 387:827-30. [PMID: 9194566 DOI: 10.1038/42990] [Citation(s) in RCA: 322] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The biosynthesis of penicillin and cephalosporin antibiotics in microorganisms requires the formation of the bicyclic nucleus of penicillin. Isopenicillin N synthase (IPNS), a non-haem iron-dependent oxidase, catalyses the reaction of a tripeptide, delta-(L-alpha-aminoadipoyl)-L-cysteinyl-D-valine (ACV), and dioxygen to form isopenicillin N and two water molecules. Mechanistic studies suggest the reaction is initiated by ligation of the substrate thiolate to the iron centre, and proceeds through an enzyme-bound monocyclic intermediate. Here we report the crystal structure of IPNS complexed to ferrous iron and ACV, determined to 1.3 A resolution. Based on the structure, we propose a mechanism for penicillin formation that involves ligation of ACV to the iron centre, creating a vacant iron coordination site into which dioxygen can bind. Subsequently, iron-dioxygen and iron-oxo species remove the requisite hydrogens from ACV without the direct assistance of protein residues. The crystal structure of the complex with the dioxygen analogue, NO and ACV bound to the active-site iron supports this hypothesis.
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Affiliation(s)
- P L Roach
- The Dyson Perrins Laboratory, University of Oxford, UK
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45
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46
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Roach PL, Clifton IJ, Hensgens CM, Shibata N, Long AJ, Strange RW, Hasnain SS, Schofield CJ, Baldwin JE, Hajdu J. Anaerobic crystallisation of an isopenicillin N synthase.Fe(II).substrate complex demonstrated by X-ray studies. EUROPEAN JOURNAL OF BIOCHEMISTRY 1996; 242:736-40. [PMID: 9022704 DOI: 10.1111/j.1432-1033.1996.0736r.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Isopenicillin N synthase (IPNS) was cocrystallised with ferrous sulphate and its substrate, delta-(L-alpha-aminoadipoyl)-L-cysteinyl-D-valine (Aad-Cys-Val). Vital to the successful procedure was the maintenance of a rigorously anaerobic environment. Hanging-drop vapour-diffusion crystallisation experiments, using lithium sulphate as the precipitant produced three crystal forms. Form I crystals, with a plate habit, diffracted X-rays to at least 0.11-nm resolution at the European Synchrotron Radiation Facility and belong to the space group P2(1)2(1)2(1), with unit-cell dimensions a = 4.68, b = 7.15, c = 10.10 nm. Their asymmetric unit contains a single IPNS.Fe(II).Aad-Cys-Val complex with a solvent content of 38.5%. Form II crystals, with a hexagonal habit, diffract X-rays to at least 0.21 nm resolution at the European Synchrotron Radiation Facility and belong to the space group P3(1)21, with unit-cell dimensions a = 10.10, b = 10.10, c = 11.567 nm. Their asymmetric unit also contains a single IPNS.Fe(II).Aad-Cys-Val complex with a solvent content of 69.5%. Form III crystals, needles, do not show well-ordered diffraction. Although all three forms were initially produced in crystallisation experiments under identical conditions, appropriate micro and streak seeding allows selective crystallisation of form I or form II crystals. Extended X-ray-absorption fine-structure studies on a crystalline slurry of the form I crystals demonstrate the presence of an Fe-S(Aad-Cys-Val) bond length of 0.234 +/- 0.003 nm.
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Affiliation(s)
- P L Roach
- Dyson Perrins Laboratory, University of Oxford, UK
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47
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Que L, Ho RYN. Dioxygen Activation by Enzymes with Mononuclear Non-Heme Iron Active Sites. Chem Rev 1996; 96:2607-2624. [PMID: 11848838 DOI: 10.1021/cr960039f] [Citation(s) in RCA: 529] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Lawrence Que
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455
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48
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Meyer-Klaucke W, Winkler H, Schünemann V, Trautwein AX, Nolting HF, Haavik J. Mössbauer, electron-paramagnetic-resonance and X-ray-absorption fine-structure studies of the iron environment in recombinant human tyrosine hydroxylase. EUROPEAN JOURNAL OF BIOCHEMISTRY 1996; 241:432-9. [PMID: 8917440 DOI: 10.1111/j.1432-1033.1996.00432.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Isoforms (1-4) of human tyrosine hydroxylase (TH) have been expressed in Escherichia coli and purified as apoenzymes (metal-free). Apo-human TH binds 1.0 atom Fe(II)/enzyme subunit, and iron binding is associated with an immediate and dramatic (40-fold) increase in specific activity. For X-ray absorption fine structure (XAFS) and electron paramagnetic resonance (EPR) measurements the apoenzyme was reconstituted with 56Fe and for Mössbauer measurements with 57Fe. XAFS measurements at the Fe-K edge of human TH were performed on the native form [Fe(II)-human TH], as well as after addition of stoichiometric amounts of the substrate tetrahydropterin, the inhibitor dopamine and of H2O2. The addition of dopamine or H2O2 oxidizes the ferrous iron of the native human TH to the ferric state. In both redox states the iron is octahedrally coordinated by low-Z backscatterers, thus sulfur coordination can be excluded. From the multiple scattering analysis of the EXAFS region is was surmised that part of the iron coordination is due to (3 +/- 1) imidazols. Addition of tetrahydropterin does not significantly change the iron coordination of the Fe(II) enzyme. The Mössbauer results confirm the valence states and the octahedral coordination of iron as well as the exclusion of sulfur ligation. Both the EPR spectra and the Mössbauer magnetic hyperfine pattern of dopamine- and H2O2-treated native human TH, were analyzed with the spin-Hamiltonian formalism. This analysis provides significantly different features for the two forms of human TH: the ferric iron (S = 5/2) of the H2O2-treated form exhibits a rhombic environment while that of the dopamine-treated form exhibits near-axial symmetry. The specific spectroscopic signature of dopamine-treated human TH, including that of an earlier resonance-Raman study [Michaud-Soret, I., Andersson, K. K., Que, L. Jr & Haavik, J. (1995) Biochemistry 34, 5504-5510] is most likely due to the bidentate binding of dopamine to iron.
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Affiliation(s)
- W Meyer-Klaucke
- Institut für Physik, Medizinische Universität zu Lübeck, Germany
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49
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Tan DS, Sim TS. Functional analysis of conserved histidine residues in Cephalosporium acremonium isopenicillin N synthase by site-directed mutagenesis. J Biol Chem 1996; 271:889-94. [PMID: 8557701 DOI: 10.1074/jbc.271.2.889] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The isopenicillin N synthase of Cephalosporium acremonium (cIPNS) involves a catalytically important non-heme iron which is coordinated credibly to histidine residues. A comparison of the IPNS genes from various microbial sources indicated that there are seven conserved histidine residues. These were individually replaced by leucine residues through site-directed mutagenesis, and the sites of mutation were confirmed by DNA sequencing. The seven mutant genes were cloned separately into the vector pET24d for expression in Escherichia coli BL21 (DE3), and the proteins were expressed as soluble enzymes. All the resulting mutant enzymes obtained have mobilities of approximately 38 kDa, identical with the wild-type enzyme on SDS-polyacrylamide gel electrophoresis, and were also reactive to cIPNS antibodies. The enzymes were purified by ammonium sulfate precipitation and DEAE-Sephadex A-50 ion exchange chromatography, and these were analyzed for enzyme activity. A group of mutant enzymes, H49L, H64L, H116L, H126L, and H137L, were found to be enzymatically active with reduced activities of 16-93.7%, indicating that they are not essential for catalysis. Two of the mutant enzymes, H216L and H272L, were found to have lost their enzymatic activity completely, indicating that both His-216 and His-272 are crucial for catalysis. It is suggested that these histidines are likely to serve as ligands for binding to the non-heme iron in the IPNS active site. Alignment of the amino acid sequence of IPNS to related non-heme Fe(2+)-requiring enzymes indicated that the two essential histidine residues correspond to two invariant residues located in highly homologous regions. The conservation of the two closely located histidine residues indicates the possible conservation of similar iron-binding sites in these enzymes.
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Affiliation(s)
- D S Tan
- Department of Microbiology, Faculty of Medicine, National University of Singapore, Republic of Singapore
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50
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Solomon EI, Pavel EG, Loeb KE, Campochiaro C. Magnetic circular dichroism spectroscopy as a probe of the geometric and electronic structure of non-heme ferrous enzymes. Coord Chem Rev 1995. [DOI: 10.1016/0010-8545(95)01150-n] [Citation(s) in RCA: 119] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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